Primers for the detection and identification of bacterial indicator groups and virulene factors

ABSTRACT

The present invention relates to new primers for the detection of any of three important bacterial indicator groups used in food microbiology and two virulence factors, which are associated with the aetiology of several types of watery and bloody human diarrhoea. It also provides a method for subtyping the two virulence factors. Furthermore, the present invention also relates to use of the primers, as well as use of the primers in a method which enables this detection, as well as the detection of new emerging pathogenic bacteria.

The present invention relates to new primers for the detection of any of three important bacterial indicator groups used in food microbiology and two virulence factors, which are associated with the aetiology of several types of watery and bloody human diarrhoea. Furthermore, the present invention also relates to use of the primers in a method which enables this detection, as well as the detection of new emerging pathogenic bacteria.

There is a great need today for methods to secure safe sanitary (i.e. the absence of harmful bacteria) evaluation of goods for human consumption, in particular water, as well as methods for the detection of pathogen bacteria useful for e.g. clinical diagnostic. Three important target bacterial indicator groups (made of various species) currently used in food microbiology are the Enterobacteriaceae (family), Escherichia coli (E. coli; a species belonging to the Enterobacteriaceae family) and the fecal enterococci (most species of the Enterococcus genus).

The Enterobacteriaceae is a coherent well-defined taxonomic unit, which is relevant both to clinical diagnostic and to food and water routine microbiological analysis, as it includes important human pathogens and the total coliform group. Traditional microbiological methods used for the identification of this family rely on biochemical properties of isolated re-grown bacterial colonies. Only few faster alternative methods have been developed so far, and they are based on the identification of a trait or marker specific to the taxon. Sequences of 16S rRNA genes have been widely used for phylogenetic and taxonomic analysis as well as for diagnostic applications, i.e. for the detection of Enterobacteriaceae members (Mittelman et al. 1997).

The Enterobacterial Common Antigen (ECA) was first described in 1963 by Kunin et al. (Kunin 1963) and defined as a cross-reactive antigen that is detectable in all genera of Enterobacteriaceae by indirect hemagglutination and by other methods using antiserum to E. coli. It was later found to be strictly family specific with diagnostic and prophylactic potential. The only known noticeable reported exceptions are the Enterobacteriacea ECA-negative Erwinia chrysanthemi and the non-Enterobacteriacea ECA-positive Plesiomonas shigelloides, both of which have disputed taxonomic positions (see review (Kuhn et al. 1988)). The ECA is a glycophospholipid built up by an aminosugar heteropolymer linked to an L-glycerophosphatidyl residue. This surface antigen remained undetected for a long time due to its non-immunogenicity in most Enterobacteriaceae despite its general ability to act as an epitope (hapten). The genes implicated in the synthesis of ECA, rfe and rff, are clustered around 85 min on the E. coli genome (Ohta et al. 1991).

Immunology-based diagnostic tests have been developed to detect the presence of ECA for clinical applications (Malkamaki 1981) and later to monitor drinking water microbiological quality by detecting bacteria belonging to the Enterobacteriaceae family (Hubner et al. 1992). Such tests rely on the expression of the character being screened, which might be absent or poorly expressed in mutants, although most of the coding material may still remain intact. In this connection DNA-based techniques, i.e. PCR, have been successfully used to decrease the amount of false negatives in diagnostic applications, i.e. beta-glucuronidase enzyme and its coding sequence used for the detection and identification of E. coli (Feng et al. 1991). However, in order to be efficient and practical, it is important that the PCR methods that are used are robust, i.e. that they provide a strong and easily reproducible amplification, with no generation of additional product. Furthermore, the use of multiple primer sets in the same PCR reaction (i.e. multiplex PCR; two primer pairs means a duplex PCR, three primer pairs a triplex PCR etc.) is also preferable to the use of a separate PCR protocol for each of the primer sets (i.e. simplex PCR) when multiple targets are searched. This allows saving time and reagents, and thus lowering the cost of the analysis.

When applying PCR it is possible to use so called universal primers. Universal primers have the purpose of working for all variants of a given gene or DNA target. Typically the primers will be chosen in the most conserved areas of the gene, ideally identical in all variants. When no conserved identical portion can be used, two strategies can be used to accommodate the ambiguous nucleotide positions: silent mismatch and degenerate primers. In the first case, the primers are designed so that the variable nucleotide positions are placed in the primers to allow amplification to proceed although there is one or more mismatch. Typically, these ambiguous positions will be placed at the 5′ end of the primers. In the case of degenerate primers, all the ambiguous positions are accounted for, and a mix of all possible combination of the variable positions is used. This has the inconvenience of diluting the one full match primer set. However, the advantage is that it will be more efficient for highly variable genes and have more chances of functioning on new unknown variants of the target.

E. coli is a member of the Enterobacteriaceae and the main species of the thermotrophic coliform group, also called the faecal coliform group. In the UK, the Drinking Water Inspectorate advised the committee responsible for revising Report 71 (Public Health Laboratory Services 1994) that for regulatory purposes, confirmed E. coli can be regarded as faecal coliforms. Furthermore, as E. coli is viewed as the only true faecal coliform and constitutes up to 99% of all faecal coliform isolates, its detection has been recommended for the evaluation of water microbiological quality. Traditional microbiological methods have relied on the expression of specific biochemical properties such as fermenting lactose or manitol at 44° C. with the production of acid and usually gas within 24 hours, and the production of indole from tryptophane. The expression by most E. coli strains of the β-glucuronidase has also been exploited. As previously mentioned, such tests rely on the expression of the specific characteristic which may lack or be delayed among certain strains although the genes might still be present. Hence, DNA-based methods, i.e. PCR, not only will reduce the analysis time, but also reduce the amount of false negatives when a reliable specific target gene or signature sequence within the chosen gene is used. Various PCR methods have been developed for detecting E. coli based on the detection of uidA (β-glucuronidase) and lamB (maltose high-affinity uptake system) (Bej et al. 1991b), or gadAB (glutamate decarboxylase) (McDaniels et al. 1996) which was also successfully used for pathogenic E. coli (Grant et al. 2001).

Enterococcus is catalase-negative Gram-positive facultative anaerobic bacteria, and the two major species of interest to humans are Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium). They are very common intestine commensal but are also responsible for nosocomial bacteremia, surgical wound infection, endocarditis and urinary tract infection. Most infections are caused by E. faecalis, which has virulence genes, whereas E. faecium has not but is more often resistant to glycopeptides (vancomycin and teicoplanin). Because of the lack of biochemical diversity between enterococcal species, reliable identification using traditional microbiological tests has proven to be difficult. This has become a problem for infection control purposes, as accurate species identification is required for the appropriate antibiotic treatment of enterococci infections. For example, E. faecalis usually are susceptible to ampicillin whereas vancomycili-resistant E. faecium also express high levels of resistance to β-lactams.

In addition of being clinically relevant species, E. faecalis and E. faecium are the two main species of the faecal enterococci indicator group used for the microbiological assessment of food and water. PCR methods have been developed to detect other enterococcal species using for example the vanC-1, vanC-2 and vanC-3 genes of E. gallinarum, E. casseliflavus and E. flavescens respectively, coding for their specific intrinsic low resistance to glycopeptides (Dutka-Malen et al. 1995). Other nucleotide based methods have been using housekeeping genes such as 23S rRNA gene (Betzl et al. 1990), super oxide dismutase gene (Bergeron et al. 1999) or randomly selected specific DNA sections (Cheng et al. 1997) for the specific detection of E. faecalis and E. faecium. Finally, tuf coding for the elongation factor EF-Tu has been used for the identification of the Enterococcus genus (Ke et al. 1999). However, none of these methods managed to simultaneously detect E. faecalis and E. faecium nor did they use a specific gene for the detection. House keeping genes were used which reduces the chances of developing a robust PCR or to further develop a multiplex method.

In addition to the detection of bacterial indicator groups, in which different species or sub-species (may) share similar genes for the coding of specific virulence factors, methods to detect the virulence factor themselves are important. Two virulence factors found in e.g. enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) are Shiga toxin (Stx) encoded by the gene stx and Intimin encoded by the gene eae. These two virulence factors are known as the two main virulence factors associated with the onset of human diarrhoea symptoms by these bacterial pathogens (i.e. EPEC and EHEC).

The Shiga toxin class, as indicated by its name, was first discovered in Shigella dysenteriae type 1 bacteria. A similar toxin was later discovered in E. coli, characterized as cytotoxic to vero cells and named Vero toxin (VT). The group of E. coli producing VT was accordingly named VTEC. The VT was later shown to be related to Shiga toxin, which prompted some authors to rename it Shiga like toxin (SLT), and the term SLTEC was used to describe the bacterial group (i.e. E. coli) producing it. As it became more evident that all Shiga toxins are related, a new genetic nomenclature was proposed and widely accepted (and is the one we use in the present study), and consequently this group of E. coli is now referred to as Shiga toxin producing E. coli (STEC).

Many variants of the stx gene have been described and new ones are still characterized. They have been classified in 2 main groups according to their sequence similarity. The first, stx₁, is found in STEC and are almost identical to the shiga toxin genes of S. dysenteriae type 1, stx. The second group, stx₂ and variants, is the most divergent and comprises sub-groups which appear to be found in host-adapted strains and other species than E. coli, and also encode for the most potent shiga toxin for humans. Both stx₂ and stx_(2c) are mainly hosted by STEC associated with the aetiology of severe human diarrhoea, whereas stx_(2d) has been isolated in STEC of both human and cattle origin. Finally, stx_(2e) are found in porcine E. coli while stx_(2f) are found in E. coli hosted by birds. Although Stx2e and Stx2f toxins seem to be adapted to their respective hosts, they both have been associated with human disease. Combination of different stx variants can be found in a same bacteria as illustrated by the case of a patient with three different STEC serotypes, each of which was hosting Stx1, Stx2 and Stx2c. Cattle are considered to be the main reservoir of STEC with 50 to 95% of the animals found to be host, although many other domestic animals were also found to host STECs. It was also shown that bacteria carrying stx genes were isolated from marine waters and are commonly found in rivers. Although not all Stx-producing bacteria can have phage induced, all stx genes are considered to be phage borne, including for S. dysenteriae serotype 1. In this connection, Shiga toxin-converting bacteriophages are commonly isolated. in sewage and were shown to play an important role in the emergence of new STEC variants. These findings illustrates how ubiquitous Shiga toxins are in our environment spanning from land to sea and air, with the intrinsic potential of horizontally spreading to new bacterial hosts.

The Shiga toxin is an A-B toxin type formed of the association of 5 B subunits structured in a ring-alike shape, and one A subunit on top of the ring. The ring is responsible for the recognition and attachment to the eukaryotic Gb3 globotriaosylceramide cell receptor of the toxin whereas the A subunit is the active toxic component that inhibits protein synthesis by removing an adenine from the 28 S rRNA. The two subunits are encoded by two genes organized in an operon in which the B subunit is more transcribed than A, enabling the final molecular ratio of 1/5 for the whole toxin. The stxA gene varies in length from 948 bp for stxA₁ to around 960 bp for stxA₂, and the “theoretical” maximum length after alignment of all variants is 967 bp and is used as the reference template for numbering the primers as shown in FIG. 9. The B subunit is 267 bp in length. As more stxA sequences were described than stxB, and as stxA is longer, we chose the latter (i.e. stxA) for the development of universal primers to detect the presence of stx.

Although the first and main STEC serotype associated with the onset of human disease is O157:H7, over a 100 serotypes have been recognized and thus, the importance of developing methods for detecting them has been emphasized (World Health Organization 1998). The STEC serotype associated with the development of human haemolytic uraemic syndrome (HUS) might vary from a country to another as shown in a recent Australian survey in which non of the 98 HUS cases identified over 4 years were associated to O157:H7. Similarly, in another Australian study, no O157:H7 were isolated among the 23 STEC isolated from bovine faecal samples. Non-O157 STEC were possibly previously underestimated because of the use of diagnostic methods targeting typical phenotypic characteristics of the O157:H7 serotype such as delayed sorbitol fermentation and lack of glucuronidase activity rather than toxin detection. These tests were developed to enable mass screening by routine laboratory but will obviously miss many STEC including atypical O157 isolates. The same critic can be made for serological diagnostic tests, which are specific to the serotype, i.e. O157 detection methods. Other immunological diagnostic methods targeting Shiga toxins have been developed but rely on toxin expression and lack the analytical flexibility DNA-based methods have. To circumvent the unreliability of phenotypic expression, it is clear that a DNA-based method able to detect all variants of the gene encoding Shiga toxin is needed when evaluating human health risk of environmental samples or when identifying aetiological agents of human gastro-enteritis. Although various universal primer pairs for the detection of stx have been described in the literature (see FIG. 1 and Table 4), few are able to detect all variants or have been used in a multiplex assay.

The eae gene (E. coli attaching and effacing) encodes Intimin of pathogenic E. coli producing the typical A/E (attaching-and-effacing) histopathology in infected patients. Five different types have been described: α, β, γ, δ & ε. The open reading frame varies in length from 2820 bp for intimin α and β to 2847 bp for intimin ε. Intimin is a protein involved in the intimate adherence of the bacterium to the epithelial cell membrane of the host's gut. In an experiment with human volunteers, intimin was proven to be necessary for the full development of diarrhoea caused by EPEC. The eae gene is found in the so-called locus of enterocyte effacement (LEE) pathogenecity island of both EPEC and EHEC. The location of LEE on the chromosome rather than on a plasmid, which is often the case for several other virulence factors, is beneficial in terms of stability of that DNA segment. Plasmid loss during sub-culturing has been reported and demonstrates that pathogenic plasmid borne molecular markers might be unreliable.

Several patents disclose methods to detect harmful bacteria. U.S. Pat. No. 6,207,818, U.S. Pat. No. 6,060,252, U.S. Pat. No. 6,054,269 and U.S. Pat. No. 5,298,392 all describe the amplification and detection of such harmful bacteria, however, the methods either detect different indicator markers/groups (i.e. bacteria) and/or different virulence markers/factors (i.e. gene(s)) compared to what is disclosed in the present application. Furthermore, the methods used in these patents do not combine the Enterobacteriaceae indicator group with virulence markers.

U.S. Pat. No. 6,218,110, U.S. Pat. No. 6,165,724 and U.S. Pat. No. 5,795,717 use oligonucleotides in PCR protocols to detect STEC bacteria. However, as opposed to what is disclosed in the present application, they use 2 or more sets of primers for the detection of stx and all variants.

U.S. Pat. No. 5,652,102 use oligonucleotides in a multiplex PCR protocol to detect STEC bacteria, however, as opposed to what is disclosed in the present application, the primer pairs are claimed to be specific to the E. coli O157 serogroup and no indicator group is associated to the method.

U.S. Pat. No. 5,994,066, U.S. Pat. No. 5,786,147 and U.S. Pat. No. 5,693,469 use a “housekeeping gene” like rRNA and/or probe technology (as opposed to PCR) to detect various bacteria, and is thus more limited and/or cumbersome than the method disclosed in the present application.

Two articles by Fratamico et al. (Fratamico et al. 1993) disclose the use of multiplex PCR protocols using universal primers for stx; however, these primers are not able to detect the eae to gene and variants. Furthermore, these protocols use mismatched universal primer pairs developed by Karch et al. (Karch and Meyer 1989), which was later reported not to detect all variants originally claimed.

Osek et al. (Osek 2001) have reported the development of a multiplex PCR for the detection of ETEC and E. coli by targeting the genes elt and est, as well as the E. coli specific stress protein gene uspA, whereas Grant et al. (Grant et al. 2001) have reported the use of multiplex PCR for the detection of STEC and E. coli by targeting stx1, stx2 and gadAB. However, both Osek and Grant are using multiplex PCR targeting a smaller indicator group compared to what is done according to the present invention.

Enterobacteriaceae has been proposed for the replacement of the currently used faecal coliform (FC) indicator group in the microbial quality assessment of water. The definition of the FC indicator group, and which species to include in it, has been the focus of much debate. Coliform isolation methods were often used to define this group albeit the lack of a rational taxonomic basis and none of the coliforms can function as reliable markers for all enteric pathogens (Leclerc et al. 2001). In contrast to FC, that was created to fit the human concept of indicator/index group, the family Enterobacteriaceae is a consistent and well-defined phylogenic entity, which is easier to define than the FC indicator group. Also, the choice of Enterobacteriaceae makes it possible to include the detection of important water-born pathogens such as Salmonella or Shigella, which are not detected by the FC microbiological tests currently in use. Thus, the use of Enterobacteriaceae would constitute a safer indicator marker for assessing the efficiency of food and water treatment. Furthermore, while E. faecalis and E. faecium both commonly were considered to be harmless commensal of the human digestive tract, they have recently emerged as important aetiological agents for various nosocomial diseases. Aside from virulence factors they have acquired a steadily increasing pool of resistance determinants to antibiotics (ampicillin, aminoglycosides and glycopeptides) which turned them into resilient potentially life threatening pathogenic bacteria. Thus, similar to E. coli, they have cumulated relevant traits as being the major members of traditional indicator groups important for water surveillance, and are potential pathogens important to be identified in the clinical world. With regard to virulence factors, the detection of intimin and the shiga encoding genes are considered important, as they are highly associated with the onset of human diarrhoea caused by e.g. the EHEC, EPEC and Shigella dysenteriaeae bacteria. Furthermore, as many species or sub-species of bacteria often share similar genes for the coding of specific virulence factors (e.g. stx and eae), and because these virulence factors often are located on mobile elements, there exist a need for new primers/methods to detect these specific virulence genes in various bacteria groups.

It is therefore an object of the present invention to provide new primers, as well as use of the primers in a method, in order to detect relevant bacteria indicator groups, as well as virulence factors, useful for both clinical diagnostic and for the sanitary evaluation of goods for human consumption. Furthermore, it is also an object of the present invention to enable the detection of new emerging bacteria with specific virulence genes. These objects have been obtained by the present invention, characterized by the enclosed claims.

The present invention relates to several new, oligonucleoticle primers and universal degenerate oligonucleotide primers according to any of the sequences SEQ ID NO 1 to SEQ ID NO 32 (see Table 2) for the detection of any of three important bacterial indicator groups used in food microbiology, as well as two virulence factors which are associated with the aetiology of several types of watery and bloody human diarrhoea. The three target indicator groups are 1) the Enterobacteriaceae, which includes the total coliform group, 2) the species E. coli, a member of the Enterobacteriaceae family, and 3) the two species E. faecalis and E. faecium belonging to the faecal enterococci indicator group. The target virulence factors are Shiga toxin (Stx) encoded by the gene stx and Intimin encoded by the gene eae. These two virulence factors are found in EPEC and EHEC among others, and recognized as the two main virulence factors associated with the onset of the human diarrhoea symptoms by these bacterial pathogens. Shiga toxin is found in Shigella dysenteriae and has been identified in emerging pathogens such as Shigella sonnei and Citrobacter rodentium, whereas Intimin has been identified in emerging pathogens such as Hafnia alvei. The universal primers according to the present invention were designed in an effort to enable detection of all gene variants of the virulence factors, independently of the bacteria hosting them. Hence, the primers according to the present invention enable the possible detection of new emerging pathogenic bacteria.

The present invention also relates to use of the primers according to the present invention, wherein the primers have the sequences according to any of the sequences as defined in SEQ ID NO 1 to SEQ ID NO 32.

The present invention further discloses the association of indicator markers with virulence markers in a robust and reliable multiplex PCR for the targets of interest wherein, compared to currently used technology, indicator markers also useful for clinical applications are used. Thus, according to another aspect, the present invention also relates to use of the primers according to the present invention, in a method preferably based on multiplex PCRs (i.e. triplex PCR or multiplex PCR depending on the objectives of the analysis and the amount of information needed) which enables the detection of any of three important bacterial indicator groups used in food microbiology and the two virulence factors which are associated with the aetiology of several types of watery and bloody human diarrhoea, as well as the possible detection of new emerging pathogenic bacteria. However, and according to a further aspect of the present invention, simplex PCR may also, depending upon the analysis requirements, be used. Furthermore, and according to the present invention, the method comprise preferably a restriction enzyme digestion and a seminested duplex PCR protocol for the accurate analysis of the stx gene.

The present invention will now be described in more detail, with reference to figures and examples. However, the examples are not to be interpreted as restrictive to the scope of the enclosed claims.

FIG. 1. Comparison of the alignments of previously described primers aiming at the detection of stx genes and their variants; +, forward primer; −, reverse primer; arrows are also indicating the direction of the primers.

FIG. 2. Comparison of the alignments of previously described primers for the detection of eae genes and their variants; +, forward primer; −, reverse primer; arrows are also indicating the direction of the primers.

FIG. 3. Agarose (1.7%) gel electrophoresis of mixtures of DNA templates showing the specificity of the multiplex reactions and the optimization of MgCl₂ and primer concentrations. Lanes: 1, negative control; 2 & 15, DNA size markers; 3, 5, 7, 9, 11 and 13, E. coli O157:H7; 4, 6, 8, 10, 12 and 14, Shigella dysenteriae; 3 to 8, 0.1 μM eae28UU18/eae748LU21 primers, 0.2 μM UstxU1/UstxL1 primers and 0.02 μM Meca202UU20/Meca633LU21 primers; 9 to 14, 0.1 μM eae28UU18/eae748LU21 primers, 0.5 μM UstxU1/UstxL1 primers and 0.05 μM Meca202UU20/Meca633LU21 primers.

FIG. 4. Agarose (1.7%) gel electrophoresis of mixtures of DNA templates showing the specificity of the multiplex reactions and the optimization of MgCl₂ concentrations. Lanes: 2, negative control; 3 & 14, DNA size markers; 4, 7 and 10, E. coli O157:H7; 5, 8 and 11, E. coli O157:H7 with Shigella dysenteriae; 6, 9 and 12, Shigella dysenteriae.

FIG. 5. Agarose (3%) gel electrophoresis showing stx simplex PCR and subsequent Bsr I digestion for 14 different STECs strains and 3 Shigelia dysenteriae serotype 1. The detailed typing results are shown in Table 9. Lanes 1, 16, 17 & 32, DNA size markers; 2 & 3, E. coli O128:H?; 4 & 5, E. coli O113:H21; 6 & 7, E. coli O157:H7; 8 & 9, E. coli O157:H7; 10 & 11, E. coli O?: H?; 12 & 13, Shigelia dysenteriae; 14 & 15, Shigella dysenteriae; 18 & 19, Shigella dysenteriae; 20 & 21, E. coli O157:H7; 22 & 23, E. coli O157:H-; 24 & 25, E. coli O157:H?; 26 & 27, E. coli O157:H7; 28 & 29, E. coli O157:H7; 30 & 31, E. coli O157:H7;

FIG. 6A. Agarose (1.7%) gel electrophoresis showing the specificity of the triplex PCR reactions using 15 different bacterial strains. Lanes: 1, DNA size markers; 2, E. coli O128:H?; 3, E. coli O113:H21; 4, E. coli O157:H7; 5, E. coli O157:H7; 6, E. coli O?:H?; 7, Shigella dysenteriae; 8, Shigella dysenteriae; 9, Shigelia dysenteriae; 10, E. coli O157:H7; 11, E. coli O157:H-; 12, E. coli O157:H?; 13, E. coli O157:H7; 14, E. coli O157:H7; 15, E. coli O157:H7; 16, E. coli O157:H7.

FIG. 6B. Agarose (1.7%) gel electrophoresis showing results from a seminested duplex PCR performed on diluted aliquots of product of triplex PCR shown on FIG. 6A.

FIG. 6C. Agarose (1.7%) gel electrophoresis showing results from a seminested duplex PCR performed directly on the same strains used for the triplex PCR shown in FIG. 6A

FIG. 7. Agarose (1.7%) gel electrophoresis of mixtures of DNA templates showing the specificity of the simplex PCR using the Meca479UU21 and Meca722LU21 primer pair. Lanes: 2, DNA size markers; 3, E. coli environmental isolate; 4, E. coli environmental isolate; 5, Pseudomonas aeruginosa; 6, Pseudomonas fluorescence; 7, E. coli O26:K60 (EPEC); 8, E. coli O44:K74 (EPEC); 9, Aeromonas hydrophila; 10, Aeromonas sobria; 11, Shigella flexneri serotype 2B; 12, Shigella sonnel; 13, Enterococcus faecalis; 14, Enterococcus faecium; 15, Shigella dysenteriae serotype 1; 16, Shigella dysenteriaea serotype 1.

FIG. 8. Agarose (1.7%) gel electrophoresis of simplex stx optimization for MgCl₂ and annealing temperature (T_(a)). Lane 1, DNA size markers; Lanes 2 to 16, EHEC O113:H21; Lanes 2, 5, 8, 11 and 14, 1.5 mM MgCl₂; Lanes 3, 6, 9, 12 and 15, 2 mM MgCl₂; Lanes 4, 7, 10, 13 and 16, 3 mM MgCl₂; Lanes 2, 3 and 4, 47.0° C. T_(a); Lanes 5, 6 and 7, 48.5° C. T_(a); Lanes 8, 9 and 10, 52.1° C. Ta; Lanes 11, 12 and 13, 54.0° C. T_(a); Lanes 14, 15 and 16, 57.8° C. T_(a); All PCR reactions have 0.1 μM Ustx primer and 0.01 μM stx2f primers.

FIG. 9. Alignment of different stx primers/sequences.

FIG. 10. Alignment of different eae primers/sequences.

The present invention relates to oligonucleotide primers for the detection and partial characterisation of relevant bacteria useful for both clinical diagnostic and for the sanitary evaluation of goods for human consumption, in particular water. It has a DNA-based approach to identify some virulence factors associated with the aetiology of human diarrhoea, as well as species and family. Since different species or sub-species share similar genes for the coding of the specific virulence factors, the conserved parts of the sequence of some virulence genes were used to develop PCR primers universal for the targeted pathogenic trait (i.e. universal primers). Sequence variability within the PCR product obtained by use of the primers according to the present invention, can then be exploited for identification of the species or sub-species.

The choosing of either simplex PCR or multiplex PCR will depend upon the objectives of the analysis, as well as the amount of information needed. Routine microbiological control of food, and in particular water, will preferably (only) use the multiplex PCR, i.e. the quadruplex PCR protocol according to one embodiment of the present invention (see example 2), for detecting bacterial indicators, although positive samples might further be analysed with the triplex PCR (see example 1) to assess the presence of virulence factors. When analysing clinical samples, the multiplex PCR, i.e. the triplex PCR protocol according to another embodiment of the present invention, would be chosen for samples originating from patients with diarrhoea, although the quadruplex PCR might be required in other situations where E. faecium or E. faecalis is suspected and needs to be differentiated from Enterobacteriaceae. Thus, when desired, a more refined analysis using another test sample from the same source can be used for a second round of identification after a positive first round in order to obtain more information. Furthermore, the stx PCR product, may be further analysed by for example using a specific set of nested primers (to perform a second multiplex PCR using the product of the first PCR), specific probes or restriction enzymes. According to the present invention, restriction enzymes are used for this sub-typing, preferably after a simplex or triplex PCR amplification comprising the stx gene, (see example 3). According to the present invention, a set of seminested primers are used to differentiate stx₁ from stx₂ either after a simplex PCR amplification of the stx gene or a triplex PCR comprising the amplification of the stx gene or directly from a sample (see example 4).

The virulence genes coding for the chosen pathogenic traits are located on, or associated with, mobile elements which favours inter-species horizontal transfer and the emergence of new pathogens. One of the goals according to the present invention is that the “universal” mode of design of the primers, using degenerate rather than mismatched primers, will provide a tool for the monitoring of these mobile virulence elements thus making possible their detection, including new variants, in previously unknown bacterial hosts. The various bacterial groups and specific virulence genes targeted by use of the primers according to the present invention are presented in Table1. All 42 stx sequences and 14 eae sequences used in this work are shown in FIGS. 9 and 10 respectively TABLE 1 Multiplex gene targets and their known hosts GenBank Higher taxon Gene/marker accession no. Taxonomic unit Reference Enterobacteriaceae Shiga toxin sub-unit A X67514 Citrobacter freundii (Schmidt et al. 1993) (stxA) M19473 Escherichia coli stx₁ (Jackson et al. 1987) L04539 (EHEC) (Paton et al. 1993a) AF125520 Escherichia coli stx₂ (Plunkett, III et al. 1999) AJ249351 (EHEC) (Muniesa et al. 2000) AJ010730 (Schmidt et al. 2000) Z50754 Enterobacter clocae (Paton and Paton 1996) Serratia marcessens (Paton and Paton 1997) M19437 Shigella dysenteriaea (Strockbine et al. 1988; Unkmeir AJ271153 and Schmidt 2000) AJ132761 Shigella sonnei (Beutin et al. 1999) Intimin (eae) AF022236 Escherichia coli (EHEC/ (Elliott et al. 1998) U60002 EPEC) (Agin et al. 1996) Z11541 (Yu and Kaper 1992) X60439 (Beebakhee et al. 1992) L11691 Citrobacter rodentium (Schauer and Falkow 1993) (formerly C. freundii biotype 4280) L29509 Hafnia alvei (Frankel et al. 1994; Ridell et al. 1994; Albert et al. 1992; Albert et al. 1991) Glutamate decarboxylase M84024 Escherichia coli (Smith et al. 1992) (gadAB) M84025 Enterobacterial common S75640 Enterobacteriaceae (Kuhn et al. 1988; Ohta et al. antigen (rfe) AF233324 1991) Enterococcus Chromosomal determinant AF152237 Enterococcus faecalis (An et al. 1999) (eep) involved in the production of the peptide sex pheromone cAD1 Aminoglycoside acetyl L12710 Enterococcus faecium (Costa et al. 1993) transferase (aac(6′)-Ii)

As it can be seen from Table 1, the largest taxonomic unit to be detected by the primers according to the present invention is the bacterial family Enterobacteriaceae. Another important indicator group is the faecal enterococci, including the two major species of importance to humans E. faecalis and E. faecium, which are specifically detected. Furthermore, the primers according to the present invention was also developed to detect all variations of the genes encoding Intimin and Shiga toxin, since these factors are associated with the onset of human diarrhoea caused by EPEC, EHEC, Shigella dysenteriaeae and various emerging pathogenic bacteria. In particular, these virulence factors have been recognized as the most important for the onset of clinical symptoms in humans infected by STEC (Law 2000).

In the present invention, and as it can be seen from Table 1, the genes rfe (implicated in the synthesis of ECA), eae and stxA were used to develop universal primers for the specific detection of the Enterobacteriaceae group by PCR. According to the knowledge of the present inventors, the use of the gene rfe in order to detect Enterobacteriaceae has not been described previously. When included in the multiplex PCR, the rfe pair of primers will have the advantage of also acting as a positive control for the PCR reaction in some experimental conditions, such as when testing a sample known to contain E. coli (i.e. faeces sample). Furthermore, even though the two genes stx and eae have been extensively used to develop PCR protocols, a need to develop universal primers for clinical diagnostic has been reported in the literature. In addition, the universal primers developed for stx (Ustx) (i.e. the A subunit encoding gene of stx) and eae according to the present invention, have the advantage of being more robust than the few ones already described in the literature, and were designed to work in a multiplex PCR. Also, the use of only one primer pair for the detection of all stx variants (which is the case with the universal primers according to the present invention) as opposed to 2 or 3 primer pairs which is the case in the currently used technology, increases the robustness of the multiplex PCR, as well as the possibility of including more targets to the method. Furthermore, the unique association of Enterobacteriaceae as an indicator marker with virulence markers is useful to help bridge the notions of indicator and index markers.

According to the present invention the chromosomal determinant eep (An et al. 1999) (involved in the production of the peptide sex pheromone cAD1 which induces a mating response from E. faecalis donors carrying the haemolysin/bacteriocin (cytolysin) plasmid pAD1) was used to develop primers for the specific detection of E. faecalis (Table 1), and according to the knowledge of the present inventors, the eep determinant has never been used previously in a PCR protocol as a target for identification of E. faecalis. Various sex pheromone are produced for the specific induction of mating response by donors carrying the corresponding specific plasmid, but all sex pheromones appear to be regulated by the eep chromosomal determinant. Also, and in accordance with the present invention, another chromosome located antibiotic resistance gene for the specific detection of E. faecium has been used, the aminoglycoside acetyl transferase aac(6′)-Ii (Table 1) (Costa et al. 1993), which confers intrinsic low resistance to aminoglycosides (kanamycin, gentamycin).

Two authors, Lin Z. and Read S. C. (Lin et al. 1993;Read et al. 1992) have developed PCR methods which use a forward primer overlapping part of the forward Ustx used by the present inventors but use different reverse primers, thus generating amplicons of a different length. Moreover the overlapping forward primers they use have two mismatched positions, whereas the present inventors use degenerate, as well as longer primers. These last two points are important when evaluating robustness of the method and use of these primers in a multiplex PCR. Furthermore, Lin and Read performed only simplex PCR.

Karch (Karch and Meyer 1989) developed a simplex PCR which was later included in multiplex PCR protocols (Fratamico et al. 1993;Fratamico and Strobaugh 1998;Nagano et al. 1998) in which the reverse primer is complementary to a part of the Ustx forward primer of the present inventors. Again, two mismatches are observed with the Karch primer as shown in FIG. 1. Paton et al. in the simplex PCR they developed, (Paton et al. 1993b), used an overlapping degenerate perfect match to the reverse primer, although they used a different forward primer. Finally, Yamasaki S. described a simplex PCR (Kobayashi et al. 2001;Yamasaki et al. 1996) in which both forward and reverse primers are overlapping those of the present technology thus generating an amplicon of almost the same size (5 nucleotide less). The aim and the claim of all these protocols are to detect all variants of the stx gene using a single pair of primers. Few studies have compared and tested extensively such protocols, but two publications (Bastian et al. 1998) among which a study of the latest gene variant stx_(2f) (Schmidt et al. 2000), agree in finding that only Lin (Lin et al. 1993) achieves detection of all variants. A closer study of the reverse primers used by Paton and Yamasaki (Paton et al. 1993b;Yamasaki et al. 1996) indicates they would probably also fail because of a on nucleotide insert in the Stx2f variant symbolised by the gap in FIG. 1. To compensate for this gap we have, according to the present invention, extended the notion of degenerate primers by adding an overlapping primer pair with a perfect match to the Stx2f variant. Although it looks like an extra pair of primers, it is only one more combination to cover all the possible ambiguous positions for the same primer pair location on the stx sequence.

All the primers according to the present invention may also be used in simplex PCR protocols, and in particular the primers designed for detecting Enterobacteriaceae, E. faecium and E. faecalis. Also, all primers according to the present invention were designed using the open reading frames of the targeted genes which allows the technology to be used with RNA based amplification techniques such as NASBA (Organon Technika).

The new primers and universal degenerate primers according to the present invention were designed with the help of Oligo 6 (Molecular Biology Insights, Inc. USA) software for windows and/or designed manually using the alignments results. Primers and degenerate universal primers were designed to enhance unknown variant detection and integrate them in multiplex PCR protocol. All primers designed and used in the method according to the present invention were compared with primers described previously in the literature. Results for stxA and eae gene alignments, along with primers used in the method according to the present invention and primers previously described in the literature, are shown in FIGS. 9 and 10. A summary of FIG. 9 to compare the Ustx (i.e. universal stx) degenerate primer pair with the most relevant primer pairs used in other PCR protocols, also aiming at the detection of all stx variants with a single pair of primers, is shown in FIG. 1. In a similar way, FIG. 2 summarises the most relevant previously described primers for the detection of the eae gene.

Optimization of the triplex PCR developed to simultaneously detect Enterobacteriaceae and the presence or absence of any variants of staA and eae genes are presented in FIGS. 3 and 4. Various primer pairs were designed according to their potential compatibility in a multiplex PCR, and special care was given to the design of the degenerate primers. Simplex PCR for all primer pairs were first optimized independently by varying physical and chemical conditions such as annealing temperature and primer concentration and were then tested for specificity. Multiplex PCR was then optimized varying annealing temperature, primer concentration and also by testing various additives or facilitators such as DMSO, glycerol, bovine serum albumin, formamide and MgCl₂ which are reported helpful for multiplex PCR. We found that only an increase of MgCl₂ improved the reaction as shown in FIGS. 3 and 4 although the other PCR facilitators may still be helpful when analysing complex samples (i.e. faeces). A list of all primers designed and used in connection with the method according to the present invention is presented in Table 2. The international nomenclature for ambiguous bases used for the degenerate positions in the primers is shown in Table 3. TABLE 2 List of primers Gene Primers (5′-3′) SEQ ID Ta ° C. Location Amp(bp) stxA₁ & UstxU1 TRTTGARCRAAATAATTTATATGTG 1 52.1 279-303* 526-7 stxA₁, UstxL1 MTGATGATGRCAATTCAGTAT 2 784-805* (stxA₁) universal UstxL2 CMTGATGATGRCAATTCAGTAT 3 783-806* 523-4 (stxA₂) stxA_(2t) UstxU3 AATGGAACGGAATAACTTATATGT 4 49.0 279-303* 523 UstxL3 GGTTGAGTGGCAATTAAGGAT 5 784-804* StxA₁ nestx1U GTACAACACTKGATGATCTC 31 49.6 327-347* 200 UstxL1 MTGATGATGRCAATTCAGTAT 2 784-805* StxA₂ nestx2U TGACRACGGACAGCAGT 32 54.3 114-130* 410 UstxL1 MTGATGATGRCAATTCAGTAT 2 784-805* eae intimin eae626UU21 ATTATGGAACGGCAGAGGTTA 6 68 626-647* 207 eae812LU21 TGAAGACGTTATAGCCCAACA 7 812-833* eae626UU21 ATTATGGAACGGCAGAGGTTA 6 60 626-647* 351 eae956LU21 GGCGCTCATCATAGTCTTTCT 8 956-977* eae28UU18 ACCCGGCACAAGCATAAG 9 53.4 28-45* 741 eae748LU21 CGTAAAGCGRGAGTCAATRTA 10 748-768* eae28UU18 ACCCGGCACAAGCATAAG 9 51.8 28-45* 949 eae956LU21 GGCGCTCATCATAGTCTTTCT 11 956-977* eae28UU18 ACCCGGCACAAGCATAAG 9 54.0 28-45* 805 eac812LU21 TGAAGACGTTATAGCCCAACA 7 812-833* rfe for ECA Meca479UU21 TGGATATGGTGGCGATTATGT 12 53.2 479-499  261 specific for Meca722LU18 TCCAGGCMCGCTTAATGC 13 722-739  264 Enterobacteriaceae Meca722LU21 CYTTCCAGGMCGCTTAATGC 14 722-742  Meca582UU18 TTCCCGYCAGGCRTTTGT 15 55 582-599  265 Meca826LU21 CMGGYAWTGGTTGTGTCATCR 16 826-846  Meca202UU20 GGGTTRTCCWGCGTCTCRTT 17 58.6 202-223  452 Meca633LU21 TATTCTGCCRKYACGCCWAYK 18 633-653  gadA & gadB gad259U21 AAAGAAGAATATCCGCAATCC 19 55 259-279  160 glutamate gad402L17 GCCATTTCATCGCCATC 20 402-418  decargoxylase gad658U19 CCACAACCGCTGCACGATG 21 60 658-676  135 of E. coli gad772L21 CAGGCGGAAGTCCCAGACGAT 22 772-792  eep, Chromosomal gene efam1U AATGCCGTGGGTAATGTGGTT 23 60 855-875  494 involved in the efam1L GGCTTTTCGGGGTTCTTCTG 24 1329-1348  production of the efam2U TTGAGTTAAATGCCGTGGGTA 25 53 257-277  284 peptide sex pheromone efam2L CATGGGTCCCGCAAAG 26 525-540  cAD1 of Enterococcus faecalis aac(6′)-Ii, efuaac1U GGGGGAAGACGTATGATAATC 27 56 191-211  258 chromosomal efuaac1L TCGGGAGCTTTCTACAACTAA 28 428-448  aminoglycoside efuaac2U GGCGTATTTAACTTAGTCGT 29 58 1257-1276  212 acetyl efuaac2L TTTGCGTCTTCTCGTAATTT 30 1449-1468  transferase of Enterococcus faecium *Numeration is done using the longest hypothetical gene obtained after alignment of all variants (see FIGS. 6 and 7)

TABLE 3 Ambiguous bases nomenclature Symbol Meaning B Not A D Not C H Not G I Inosine K G or T M A or C N A or C or G or T R A or G S C or G V Not T W A or T Y C or T

According to Table 2, the following primers correspond to the following sequences:

-   -   UstxU1 corresponds to SEQ ID NO 1     -   UstxL1 corresponds to SEQ ID NO 2     -   UstxL2 corresponds to SEQ ID NO 3     -   UstxU3 corresponds to SEQ ID NO 4     -   UstxL3 corresponds to SEQ ID NO 5     -   eae626UU21 corresponds to SEQ ID NO 6     -   eae812LU21 corresponds to SEQ ID NO 7     -   eae956LU21 corresponds to SEQ ID NO 8     -   eae28UU18 corresponds to SEQ ID NO 9     -   eae748LU21 corresponds to SEQ ID NO 10     -   eae956LU21 corresponds to SEQ ID NO 11     -   Meca479UU21 corresponds to SEQ ID NO 12     -   Meca722LU18 corresponds to SEQ ID NO 13     -   Meca722LU21 corresponds to SEQ ID NO 14     -   Meca582UU18 corresponds to SEQID NO 15     -   Meca826LU21 corresponds to SEQID NO 16     -   Meca202UU20 corresponds to SEQ ID NO 17     -   Meca633LU21 corresponds to SEQ ID NO 18     -   gad259U21 corresponds to SEQ ID NO 19     -   gad402L17 corresponds to SEQ ID5 NO 20     -   gad658U19 corresponds to SEQ ID NO 21     -   gad772L21 corresponds to SEQ ID NO 22     -   efam1U corresponds to SEQ ID NO 23     -   efam1L corresponds to SEQ ID NO 24     -   efam2U corresponds to SEQ ID NO 25     -   efam2L corresponds to SEQ ID NO 26     -   efuaac1U corresponds to SEQ ID NO 27     -   efuaac1L corresponds to SEQ ID NO 28     -   efuaac2U corresponds to SEQ ID NO 29     -   efuaac2L corresponds to SEQ ID NO 30     -   nestx1U corresponds to SEQ ID NO 31     -   nestx2U corresponds to SEQ ID NO 32

As multiplex PCR methods have been previously developed for the detection of various virulence factors associated with human gastrointestinal diseases, in particular stxAB₁, stxAB₂ and variants, eae, hlyA, ipaH and eltAB, an extensive literature search have been performed to look into redundancy with prior art and is presented in Tables 4 and 5. TABLE 4 Relevant PCR protocols for the detection of virulence factors and indicator groups Pathogenic markers Indicator marker All elt Serotyping 16S Reference stx₁ stx₂ stx eae hlyA AB est invA eae rfb fli uidA uspA UidA/R Gad AB lamB lacZ rRNA (Bej et al. 1991b; Bej et al. + + + 1990; Bej et al. 1991a) (Bellin et al. 2001) + + (Call et al. 2001) + + + + (Carroll et al. 2000) + (Cebula et al. 1995) + + + (Chen and Griffiths 1998) + (Chen and Griffiths 2001) + + + (China et al. 1996) + + + (Desmarchelier et al. 1998) + (Fach et al. 2001) + (Fagan et al. 1999) + + + + (Feng and Monday 2000) + + + + + (Fratamico and Strobaugh + + + + 1998) (Fratamico et al. 2000) + + + + + (Fratamico et al. 1993) + + + (Gannon et al. 1997) + + + + (Gannon et al. 1992) + + (Grant et al. 2001) + + + (Heuvelink et al. 1995) + + + (Karch et al. 1993) + (Karch and Meyer 1989) + (Klausegger et al. 1999) + (Lang et al. 1994) + + + (Lin et al. 1993) + (McDaniels et al. 1996) + (McDaniels et al. 1996) + (Meng et al. 1996; Meng et + al. 1997) (Mittelman et al. 1997) + (Nagano et al. 1998) + + + (Olsvik et al. 1991; Olsvik + + and Strockbine 1993) (Osek 2001) + + + (Pass et al. 2000) + + + (Paton and Paton 1998) + + + + (Paton et al. 1993b) + (Paton and Paton 1998) + (Pollard et al. 1990) + + (Radu et al. 2001) + + + (Read et al. 1992) + (Tsen and Jian 1998) + + + + (Yamasaki et al. 1996) +

TABLE 5 Relevant PCR protocols for detection of E. faecalis and E. faecium Size of Target Reference & product strains, Patent PCR primer name Target gene(s) Sequence (5′-3′) (bp) Enterococcus & PCR (Ke et al. tuf, chromosomal, AAYATGATIACIGGIGCIGCICARATGGA 803 Universal, (nested) 1999), elongation AYRTTITCICCIGGCATIACCAT Universal factor EF-Tu TACTGACAAACCATTCATGATG 112 degenerate U1 AACTTCGTCACCAACGCGAAC & U2 Ent1 & Ent2 Enterococcus Multipplex (Knijff et al. ddl, chromosomal TTATGTCCCWGTWTTGAAAAATCAA 186 durans, (2), 2001), DuHifF, D-Ala D-Ala TGAATCATATTGGTATGCAGTCCG 377 Enterococcus DuR & HiR ligase for TTTTGTTAGACCTCTTCCGGA hirae peptidoglycan final synthesis step (sensitive to glycopeptides) Enterococcus Probe (Betzl et al. 23S rRNA TAGGTGTTGTTAGCATTTCG faecalis technology 1990), DB8 Enterococcus DB6 CACACAATCGTAACATCCTA faecium Enterococcus Cycle Probe (Modrusanet VanA and VanB-B2 TTAATAACCCAAAAGGCGGGAGTAGCT faecium/ Technology et al. 1999), glycopeptide TACATTCTTACAAAAAATGCGGGCATC faecalis- (CPT), 5′ vanA811L-27 resistance genes glycopeptide terminal VanB467-27 resistance labeled with [γ-³²P]-ATP. Enterococcus PCR (1) (Cheng et al. Randomly selected ACGCAACAATGGTGGTGGACA 658 faecium 1997), EM1A & B species specific TCTTGATTTGCAGTAGAGGTAATAG E. faecium DNA sequence, unknown function Enterococcus PCR (1) (Bergeron et sod, superoxide ACGCAACAATGGTGGTGGACA faecium/ al. 1999) dismutase TCTTGATTTGCAGTAGAGGTAATAG US5,994,066 Enterococcus Multiplex (Clark et vanC-1, D-Ala D-Ser GAAAGACAACAGGAAGACCGC 796 gallinarum (3) al. 1998) ligase for peptido- ATCGCATCACAAGCACCAATC (Angeletti et glycan final al. 2001) synthesis step (Satake et (constitutive low al. 1997) resistance to glycopeptides) Enterococcus vanC2-1 & -2 vanC-2 CGGGGAAGATGGCAGTAT 484 casselifavus CGCAGGGACGGTGATTTT Enterococcus vanC-3, GCCTTTACTTATTGTTCC 224 flavescens GCTTGTTCTTTGACCTTA Enterococcus Multipplex (Petrich et vanA, D-Ala D-Lac Biotin-GCTGCGATATTCAAAGCTCA 545 glycopeptide (2) al. 1999), ligase for peptido- CAGTACAATGCGGCCGTTA resistance VanA1 & VanA2 glycan final ATTGCGTAGTCCAATTC- VanA3 synthesis step Fluorescein (aquired high resistance to vancomycin & teicoplanin) EIA detection (Petrich et vanB, D-Ala D-Lac Biotin-ATGGGAAGCCGATAGTC 368 in microtiter al. 1999) ligase for peptido- GTTACGCCAAAGGACGAAC plates with (Dutka-Malen glycan final GACAATTCAAACAGACC- anti-FITC et al. 1995), synthesis step Flourescein HRP conjugate VanB1 & (aquired high resis- VanB3 tance to vancomycin) VanB4 Enterococcus- (Dutka-Malen vanA, D-Ala D-Lac GGGAAAACGACAATTGC 732 glycopeptide et al. 1995)/ ligase for peptido- GTACAATGCGGCCGTTA resistance A₁ & A₂, glycan final (Roger et synthesis step al. 1999) (aquired high (Angeletti et resistance to al. 2001) vancomycin & (Satake et teicoplanin) al. 1997) B1 & B2 vanB, D-Ala D-Lac ATGGGAAGCCGATAGTC 635 (Isenberg ligase for peptido- GATTTCGTTCCTCGACC 1998) glycan final synthesis step (aquired high resistance to vancomycin) Enterococcus Multiplex p662, C₁ & C₂ vanC-1, D-Ala D-Ser GGTATCAAGGAAACCTC 822 gallinarum (6) (Dutka-Malen ligase for peptido- CTTCCGCCATCATAGCT el al. 1995)/ glycan final (Isenberg synthesis step 1998) p662 (constitutive low resistance to glycopeptides) Enterococcus D₁ & D₂ vanC-2 & van C-3, CTCCTACGATTCTCTTG 439 casselifavus & D-Ala D-Ser ligase CGAGCAAGACCTTTAAG flavescens for peptidoglycan final synthesis step (constitutive low resistance to glycopeptides) Enterococcus E₁ & E₂ ddl_(E. faecalis), ATCAAGTACAGTTAGTCT 941 faecalis chromosomal D-Ala ACGATTCAAAGCTAACTG D-Ala ligase for peptidoglycan final synthesis step (sensitive to glycopeptides) Enterococcus F₁ & F₂ ddl_(E. faecium), TAGAGACATTGAATATGCC 550 faecium chromosomal D-Ala TCGAATGTGCTACAATC D-Ala ligase for peptidoglycan final synthesis step (sensitive to glycopeptides) Enterococcus PCR, tRNA (Baele et tRNA genes flanking AGTCCGGTGCTCTAACCAACTGAG variable species intergenic al. 2000), conserved edges AGGTCGCGGGTTCGAATCC spacer PCR, T5A & capillary T3B*(TET) electro- phoresis of amplicons Enterococcus PCR (broad (Poyart et sod, superoxide CCITAYICITAYGAYGCIYTIGARCC 480 species range) with al. 2000) dismutase ARRTARTAIGCRTGYTCCCAIACRTC Streptococcus degenerate (Poyart et Universal degenerated species & Gram primers, al. 1995), primers for the positive bacteria sequencing d1 & d2 amplification of a of the (Poyart et 480 Nu internal product and al. 1998) fragment sodA_(int) comparison to a database Best Mode

Triplex PCR: For sample analysis (i.e. the detection of bacteria), individual colonies (i.e. test samples) from Luria agar culture plates are suspended in sterile distilled water. The preparation is then either used for direct PCR of bacteria or first boiled 10 min before use for the PCR. Samples (10 μl) were amplified in 50 μl final reaction mixtures using a BioTest Biometra PCR machine. The mixtures contained 0.1 mM each dATP, dCTP, dGTP, dUTP, 1× final concentration of the 10× buffer solution and 1 U of DyNazyme II (Finnzymes) DNA polymerase per reaction. MgCl₂ is adjusted from 1.5 mM standard concentration in the 1× buffer to 3 mM final concentration. Primer concentrations are as following, 0.05 μM for Meca202UU20 and Meca633LU21; 0.5 μM for UstxU1; 0.3 μM for UstxL1; 0.02 μM for UstxU3 and UstxL3 (The triplex is not as robust when using UstxU3 and UstxL3 and should therefore not be added if the subtype Stx_(2f) is not researched); and 0.15 μM for eae28UU18 and eae748LU21. The PCR conditions consisted of 2 min preheating at 94° C. for one cycle followed by 15 s denaturation at 94° C., 30 s annealing at 57° C. and 60 s at 72° C. for 40 cycles; and 5 min final elongation at 72° C. Reaction products are separated by agarose (1.7%) gel electrophoresis with 0.5× Tris-borate-EDTA buffer and stained with ethidium bromide 0.5 μg/ml. PCR products are separated by applying seventy-five volts and 25 mA across the gel for about 1 h 30 min.

Quadruplex PCR: For direct sample analysis (i.e. the detection of bacteria) of water, the sample is centrifuged at 12000 rpm for 5 min and the pellet is re-suspended in sterile distilled water two times before it is re-suspended in a 50 μl final volume when PCR inhibitors are expected to be found. The preparation is then boiled 10 min before use for the PCR. Samples (10 μl) were amplified in 50 μl final reaction mixtures using a BioTest Biometra PCR machine. The mixtures contained 0.1 mM each dATP, dCTP, dGTP, dUTP, 1× final concentration of the 10× buffer solution and 1 U of DyNazyme II (Finnzymes) DNA polymerase per reaction. MgCl₂ is adjusted from 1.5 mM standard concentration in the 1× buffer to 3 mM final concentration. Primer concentrations are as following, 0.5 μM for efam1U and efam1L; 0.05 μM for Meca582UU18 and Meca826LU21; 0.5 μM for efuaac2U and efuaac2L; and 0.5 μM for gad259U21 and gad402L17. The PCR conditions consisted of 2 min preheating at 94° C. for one cycle followed by 15 s denaturation at 94° C., 30 s annealing at 57° C. and 60 s at 72° C. for 40 cycles; and 5 min final elongation at 72° C. Reaction products are separated by agarose (1.7%) gel electrophoresis with 0.5× Tris-borate-EDTA buffer and stained with ethidium bromide 0.5 μg/ml. PCR products are separated by applying seventy-five volts and 25 mA across the gel for about 1 h 30 min.

BsrI endonuclease restriction: The restriction endonucleases Bsr I with the recognition site ACTGG(1/−1) was purchased at New England Biolab. Digestion was performed using 16 μl PCR product (from stx simplex PCR or tiplex PCR), 10 U BsrI with the provided NEB3 buffer 1× final in a total volume of 20 μl. PCR tubes were used and digestion was carried out at 65° C. for 2h30min in the thermocycler. Reaction products are separated by agarose (3%) gel electrophoresis with 0.5× Tris-borate-EDTA buffer and stained with ethidium bromide 0.5 μg/ml. PCR products are separated by applying seventy-five volts and 25 mA across the gel for about 1 h.

Stx seminested duplex PCR: For typing (stx₁/stx₂) the product of a first positive simplex or triplex PCR (as described in Example1). The PCR product must be diluted to 10⁻³ before 5 μl sample is used in a 50 μl final reaction mixtures using a BioTest Biometra PCR machine. The mixtures contained 0.1 mM each dATP, dCTP, dGTP, dUTP, 1× final concentration of the 10× buffer solution and 1 U of DyNazyme II (Finnzymes) DNA polymerase per reaction. MgCl₂ is adjusted from 1.5 mM standard concentration in the 1× buffer to 3 mM final concentration. Primer concentrations are as following 0.1 μM for UstxL1, 0.3 μM for nestx1U and 0.05 μM for nestx2U. The PCR conditions consisted of 2 min preheating at 94° C. for one cycle followed by 15 s denaturation at 94° C., 30 s annealing at 57° C. and 60 s elongation at 72° C. for 30 cycles; and 5 min final elongation at 72° C. Reaction products are separated by agarose (1.7%) gel electrophoresis with 0.5× Tris-borate-EDTA buffer and stained with ethidium bromide 0.5 μg/ml. PCR products are separated by applying seventy-five volts and 25 mA across the gel for about 1 h. The method can also be used directly on DNA samples.

EXAMPLES Example 1 Simultaneous Detection of stx and eae Virulence Genes and Enterobacteriaceae in a Multiplex (Triplex) PCR

For sample analysis (i.e. the detection of bacteria), individual colonies (i.e. test samples) from Luria agar culture plates are suspended in sterile distilled water. The preparation is then either used for direct PCR of bacteria or first boiled 10 min before use for the PCR. Samples (10 μl) are amplified in 50 μl final reaction mixtures using a BioTest Biometra PCR machine. The mixture contains 0.1 mM each dATP, dCTP, dGTP, dUTP, 1× final concentration of the 10× buffer solution and 1 U of DyNazyme II (Finnzymes) DNA polymerase per reaction. Concentrations for MgCl₂ and primers were optimized for each multiplex and are shown in Table 6 and 7. The PCR conditions consists of 2 min preheating at 94° C. for one cycle followed by 15 s denaturation at 94° C., 30 s annealing at 57° C. and 60 s elongation at 72° C. for 40 cycles; and 5 min final elongation at 72° C. Reaction products are separated by agarose (1.7%) gel electrophoresis stained with ethidium bromide (0.5 μg/ml), and the results are shown in FIGS. 3 and 4. 0.5× Tris-borate-EDTA buffer is used for the electrophoresis. Seventy-five volts and 25 mA are applied across the gel for about 1 h 30 min to separate the PCR products. TABLE 6 Sequences of primers, conditions to perform the triplex PCR and product sizes. Product Primers MgCl₂ Gene Primers (5′-3′) Location size (bp) μM mM Ta ° C. rfe for Meca202UU20 SEQ ID NO 17 GGGTTRTCCWGCGTCTCRTT 202-223 452 0.05 3 57 ECA Meca633LU21 SEQ ID NO 18 TATTCTGCCRKYACGCCWAYK 633-653 stxA₁& UstxU1 SEQ ID NO 1 TRTTGARCRAAATAATTTATATGT  279-303* 526 (stxA₁) 0.5 stxA₂, UstxL1 SEQ ID NO 2 MTGATGATGRCAATTCAGTAT  784-805* 523 (stxA₂) 0.3 universal STXa_(2t) UstxU3 SEQ ID NO 4 AATGGAACGGAATAACTTATATGT 279-303 523 (stxA_(2t)) 0.02 UstxL3 SEQ ID NO 5 GGTTGAGTGGCAATTAAGGAT 784-804 eae eae28UU18 SEQ ID NO 9 ACCCGGCACAAGCATAAG  28-45* 741 0.15 intimin eae748LU21 SEQ ID NO 10 CGTAAAGCGRGAGTCAATRTA 748-768 *Numeration is done using the longest hypothetical gene obtained after alignment of all variants (see FIGS. 9 and 10).

The results show that only an increase in the concentration of MgCl₂ improved the reaction with an optimum concentration reached at 3 mM. Similarly optimum concentrations for the primers as indicated in Table 6 was demonstrated as shown in FIG. 3 where column 9 to 14 have optimum primer concentration. Furthermore, specificity is demonstrated in FIG. 4, as only the samples containing E. coli O157H7 produces the expected band of 741 bp that indicates the presence of the intimin gene eae. Finally, samples containing either E. coli O157H7 or Shigella dysenteriaea both show amplification products for the stx and rfe gene as expected.

Example 2 Simultaneous Detection of Enterobacteriaceae, E. coli, E. faecalis and E. faecium in a Multiplex (Quadruplex) PCR

The quadruplex PCR operational characteristics are similar to those of the triplex described in example 1 apart from specific conditions given in Table 7. TABLE 7 Sequences of primers, conditions to perform the quadruplex PCR and product sizes. Product Primers MgCL₂ Ta Gene Primers (5′-3′) Location size (bp) μM mM ° C. eep, efam1U SEQ ID NO 23 AATGCCGTGGGTAATGTGGTT 855-575 494 0.5 3 55 Chromosomal efam1L SEQ ID NO 24 GGCTTTTCGGGGTTCTTCTG 1329-1348 gene of E. faecalls rfe for ECA Meca582UU18 SEQ ID NO 15 TTCCCGYCAGGCRTTTGT 582-599 265 0.05 Meca826LU21 SEQ ID NO 16 CMGGYAWTGGTTGTGTCATCR 826-846 aac(6′)-Ii, efuaac2U SEQ ID NO 29 GGCGTATTTAACTTAGTCGT 1257-1276 212 0.5 chromosomal efuaac2L SEQ ID NO 30 TTTGCGTCTTCTCGTAATTT 1449-1468 gene of E. faecium gadAB of E. gad259U21 SEQ ID NO 19 AAAGAAGAATATCCGCAATCC 259-279 160 0.5 coli gad402L17 SEQ ID NO 20 GCCATTTCATCGCCATC 402-418

Example 3 Sub-Typing of stx by Endonuclease Restriction of stx PCR Amplification Product

The restriction endonucleases HaeII, HindIII and BsrI, purchased at New England Biolab, were chosen to obtain the appropriate restriction patterns as shown in Table 8. Endonuclease restriction is performed on the product of simplex PCR using Ustx primers (see example 6). TABLE 8 Endonuclease restriction results of the PCR amplification of stx gene variants. stx gene BsrI HaeII Hind III stx_(1c) 396, 130 526* 291, 235 stx₁ 334, 130, 62 526* 291, 235 Stx₂, Stx_(2c), Stx_(2d) 200, 193, 91, 39 369, 154 253* Stx_(2e) 200, 193, 130 369, 154 523* Stx_(2f) 200, 193, 130 331, 193 523* *No restriction

Results are shown in FIG. 5 and Table 9 for BsrI endonuclease restriction of the stx PCR amplicon. 0.5× Tris-borate-EDTA buffer is used for the electrophoresis. Seventy-five volts and 25 mA are applied across the gel for about 1 h 30 min to separate the digestion products. When using PCR products from the triplex amplification the eae amplicon (741 bp) is discriminated in two groups. Amplicons from eae α, β, δ and ε will give two fragments of 88 and 654 bp while eae γ will give three fragments of 88, 178 and 476 bp. TABLE 9 Summary of results shown in FIG. 5 (BsrI restriction of stx amplification) Lane on stxA stxA_(1c) stxA₁ All stxA₂ All stx − stxA₂ stxA_(2,2c,2d) FIG. 5 Species 523-526 396 334 200-193 130 91 Results 2 & 3 E. coli EHEC O128:H? + + − + + + stxA_(1c) + stxA_(2,2c,2d) 4 & 5 E. coli EHEC O113:H21 + − + + + + stxA₁ + stxA_(2,2c,2d) 6 & 7 EHEC E. coli O157:H7 + − + + + + 8 & 9 E. coli EHEC O157:H7 + − + − + − stxA₁ 10 & 11 E. coli EHEC O?:H? + − + − + − 12 & 13 Shigella dysenteriae + − + − + − Serotype 1 14 & 15 Shigella dysenteriae + − + − + − Serotype 1 17 & 18 Shigella dysenteriae + − + − + − Serotype 1 19 & 20 E. coli EHEC O157:H7 + − − + − + stxA_(2,2c,2d) 21 & 22 E. coli EHEC O157:H- + − − + − + 23 & 24 E. coli EHEC O157:H? + − − + − + 25 & 26 E. coli EHEC O157:H7 + − − + − + 27 & 28 E. coli EHEC O157:H7 + − − + − + 29 & 30 E. coli EHEC O157:H7 + − − + − +

Example 4 stx Seminested Duplex PCR to Differentiate stx1 and stx2 after a Simplex PCR, Triplex PCR or Directly

The seminested duplex PCR operational characteristics are similar to those of the triplex described in example 1 apart from specific conditions given in Table 10. The method can be used on 10⁻³ diluted aliquots from a triplex stx PCR as shown in FIGS. 6A and 6B or directly from individual colonies prepared as indicated in example 1 (see results in FIG. 6C). This method is very sensitive and 25 cycles are sufficient when using aliquots from a triplex PCR. The results shown in FIGS. 6B and 6C corroborate those obtained using the BsrI endonuclease restriction method shown in FIG. 5 and Table 9. TABLE 10 Sequences of primers, conditions to perform the seminested duplex PCR and product sizes Primer Product Primers MgCl₂ Gene sequence (5′-3′) Location size (bp) μM mM Ta ° C. stxA₁ & stxA₂ UstxL1 SEQ ID NO 2 MTGATGATGRCAATTCAGTAT 784-805  0.1 3 57 stxA₁ Nestx1 SEQ ID NO 31 GTACAACACTKGATGATCTC 327-347* 200 0.3 StxA₂ Nestx2 SEQ ID NO 32 TGACRACGGACAGCAGT 114-130* 410 0.05 *Numeration is done using the longest hypothetical gene obtained after alignment of all variants (see FIGS. 9 and 10).

Example 5 Simplex PCR Example for the Detection of Enterobacteriaceae

For sample analysis (i.e. the detection of bacteria), individual colonies (i.e. test samples) from Luria agar culture plates are suspended in sterile distilled water. The preparation is then either used for direct PCR of bacteria or first boiled 10 min before use for the PCR. Samples (10 μl) to are amplified in 50 μl final reaction mixtures using a BioTest Biometra PCR machine. The mixtures contains 0.1 mM each dATP, dCTP, dGTP, dUTP, 1× final concentration of the 10× buffer solution and 1 U of DyNazyme II (Finnzymes) DNA polymerase per reaction and 0.1 μM of each primer Meca479UU21 and Meca722LU21. The PCR conditions consists of 2 min preheating at 94° C. for one cycle followed by 15 s denaturation at 94° C., 30 s annealing at 57° C. and 60 s elongation at 72° C. for 40 cycles; and 5 min final elongation at 72° C. Reaction products are separated by agarose (1.7%) gel electrophoresis stained with ethidium bromide (0.5 μg/ml), and the results are shown in FIG. 6. 0.5× Tris-borate-EDTA buffer is used for the electrophoresis. One hundred volts and 40 mA are applied across the gel for about 50 min to separate the PCR products.

Simplex PCR using Meca479UU21 and Meca722LU21 is performed on various Enterobacteriaceae and non-Enterobacteriaceae species to illustrate specificity of the method. As shown in FIG. 7, no non-Enterobacteriaceae was amplified by the simplex PCR.

Example 6 Simplex PCR Example for the Detection of stx

For sample analysis (i.e. the detection of bacteria), individual colonies (i.e. test samples) from Luria agar culture plates are suspended in sterile distilled water. The preparation is then either used for direct PCR of bacteria or first boiled 10 min before use for the PCR. Samples (10 μl) are amplified in 50 μl final reaction mixtures using a BioTest Biometra T gradient PCR machine. The mixtures contains 0.1 mM each dATP, dCTP, dGTP, dUTP, 1× final concentration of the 10× buffer solution and 1 U of DyNazyme II (Finnzymes) DNA polymerase per reaction and 0.1 μM of each primer UstxU1 and UstxL1, and 0.01 μM of each primer UstxU3 and UstxL3. The PCR conditions consists of 2 min preheating at 94° C. for one cycle followed by 15 s denaturation at 94° C., 30 s annealing at 57° C. and 60 s elongation at 72° C. for 40 cycles; and 5 min final elongation at 72° C. Reaction products are separated by agarose (1.7%) gel electrophoresis stained with ethidium bromide (0.5 μg/ml), and the results are shown in FIG. 8. 0.5× Tris-borate-EDTA buffer is used for the electrophoresis. One hundred volts and 40 mA are applied across the gel for about 1 h. TABLE 11 Sequences of primers and optimum conditions to perform the simplex stx PCR and product sizes. Product Primers MgCl₂ Gene Primers (5′-3′) Location size (bp) μM mM Ta ° C. stxA₁ & UstxU1 SEQ ID NO 1 TRTTGARCRAAATAATTTATATGT 279-303* 526 (stxA₁) 0.1 3 57 stxA₂, UstxL1 SEQ ID NO 2 MTGATGATGRCAATTCAGTAT 784-805* 523 (stxA₂) 0.1 universal stxA_(2t) UstxU3 SEQ ID NO 4 AATGGAACGGAATAACTTATATGT 279-303* 523 (stxA_(2t)) 0.01 UstxL3 SEQ ID NO 5 GGTTGAGTGGCAATTAAGGAT 784-804*

Results shown in FIG. 8 demonstrate how important MgCl₂ concentration is to develop a robust PCR amplification.

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1-5. (canceled)
 6. A set of oligonucleotide primers for simultaeous use in a multiplex PCR process for the detection of bacterial indicator groups and virulence factors, said set comprising a primer directed towards the bacterial indicator group enterobacteriaceae, together at least one of the following primers: a primer directed towards the species E. faecalis, a primer directed towards the species E. faectum, a primer directed towards the species Escherichia coli, primer directed towards the virulence factors comprising all variants of the Shiga toxin, and a primer directed towards the virulence factor Itimin.
 7. A set of oligonucleotide primers according to claim 6, wherein the primer for the bacterial indicator group Enterobacteriaceae is directed towards the ire gene, the primer for the species E. faecalis is directed towards the cep gene, the primer for the species E. faecium is directed towards the gene aac (6′)-Ii, the primer for the species Escherichia coli is directed towards the gene gadA/B, the primer for the virulence factor Intimin is directed towards the eae gene and the primer for the virulence factor shiga toxin is directed towards the stx gene.
 8. A set of oligonucleotide primers according to claim 7, wherein the set comprises a primer directed towards the fre gene of the bacterial indicator group Enterobacteriaceae, together with both a primer directed towards the virulence factors comprising all variants of the Shiga toxin genes stx and a primer directed towards the eae gene of the virulence factor Intimin.
 9. A set of oligonucleotide primers according to claim 7, wherein the set comprises a primer directed towards the rfe gene of the bacterial indicator group Enterobacteriaceae, together with both a primer directed towards the gadA/B gene of the species Escherichia coli, a primer directed towards the eep gene of the the species E. faecalis, and a primer directed towards the aac(6′)-Ii gene of the species E. faecium.
 10. A set of oligonucleotide primers according to claims 6-8, wherein the primer for the virulence factor shiga toxin has a sequence selected from SEQ ID NO: 1-5
 11. A set of oligonucleotide primers according to claims 6-8, wherein the primer for the virulence factor Intimin has a sequence selected from SEQ ID NO: 6-11.
 12. A set of oligonucleotide primers according to claims 6-9, wherein the primer for Enterobacteriaceae has a sequence selected from SEQ ID NO: 12-18.
 13. A set of oligonucleotide primers according to claims 6, 7, or 9, wherein the primer for Escherichia coli has a sequence selected from SEQ ID NO: 19-22.
 14. A set of oligonucleotide primers according to claims 6, 7, or 9, wherein the primer for Enterococcus faecalis has a sequence selected from SEQ ID NO: 23-26.
 15. A set of oligonucleotide primers according to claims 6, 7, or 9, wherein the primer for E. faecium has a sequence selected from SEQ ID NO: 27-30.
 16. A set of oligonucleotide primers according to any of claim 6-9, wherein the primer for the bacterial indicator group Enterobacteriaceae has a sequence selected from SEQ ID NO: 12-18; the primer for the species E. faecalis has a sequence selected from SEQ ID NO:23-24, the primer for the species E. faecium has a sequence selected from SEQ ID NO:29-30, the primer for the species Escherichia coli has a sequence selected from SEQ ID NO: 19-20, the primer for virulence factors comprising all variants of the Shiga toxin genes str has a sequence selected from SEQ ID NO:1-5, and the primer for the virulence factor Intimin has a sequence selected from SEQ ID NO:9-10.
 17. A set of oligonucleotide primers for multiplex PCR comprising primers having the nucleic acid sequence as defined according to SEQ ID NO:15-SEQ ID NO:18 and primers selected from the group having the nucleic acid as defined according to a) SEQ ID NO:1-5, SEQ ID NO:9, SEQ ID NO 10 and optionally SEQ ID NO:31-32; or b) SEQ ID NO 19, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:29, SEQ ID NO:30
 18. A set of oligonucleotide primers according to claim 17 for triplex PCR comprising primers having the nucleic acid sequences as defined according to SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:1-5, SEQ ID NO:9, SEQ ID NO
 10. 19. A set of oligonucleotide primers according to claim 17 for quadruplex PCR comprising primers having the nucleic acid sequences as defined according to SEQ ID NO: 15, SEQ ID NO:16, SEQ ID NO 19, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:29, SEQ ID NO:30.
 20. Method for the detection of bacterial indicator groups and/or virulence factors, characterized in comprising the following steps: a) providing a test sample suspected to contain toe targeted DNA; b) amplifying the targeted DNA by the use of a set according to claims 17-19 in multiplex PCR processes; and optionally c) subtyping the str encoded virulence factor by seminested duplex PCR by the use of a set of oligonucleotide primers having the nucleic acid sequences as defined according to SEQ ID NO: 1-5, SEQ ID NO:31 and SEQ ID NO:32.
 21. Method according to claim 20, characterized in that it comprises the providing of a test sample suspected of containing the targeted DNA, amplifying the DNA by using triplex PCR with primers comprising oligonucleotides corresponding to SEQ ID NO 1-5, SEQ ID NO 9 and 10 and SEQ ID NO 17 and 18 in order to detect the presence of Enterobacteriaceae as well as the association or not of any of the two virulence genes stx and eae.
 22. Method according to claim 20, characterized in that it comprises the providing of a test sample suspected of containing the targeted DNA, amplifying the DNA by using quadruplex PCR with primers comprising oligonucleotides corresponding to SEQ ID NO 15 and 16, SEQ ID NO 19 and 20, SEQ ID NO 23 and 24 and SEQ ID NO 29 and 30, to detect the presence of Enterobacteriaceae, Escherichia coli, Enterococcus faecalis and Enterococcus faecium.
 23. Method according to the claims 20 or 21, wherein any of the primers according to SEQ ID NO 1-SEQ ID NO 5, SEQ ID NO 31 and SEQ ID NO 32 are used to detect all variants of the Shiga toxin genes stx by seminested duplex PCR.
 24. A lit for multiplex PCR for the detection of bacterial indicator groups and/or virulence factors comprising primers selected from SEQ ID NO:15-18, packaged together with primers selected from at least one of the following groups of primers: SEQ ID NO:23-24 SEQ ID NO:29-30 SEQ ID NO:19-20 SEQ ID NO:1-5 SEQ ID NO:9-10 SEQ ID NO:31-32, together with instructions for the use of said primers in multiplex PCR procedure.
 25. Method for subtyping stx encoded virulence factor by seminested PCR, characterized in comprising the following steps: a) providing a test sample suspected to contain the targeted oligonucleotide sequence; d) subtyping the stx encoded virulence factor by seminested PCR by the use of a set of oligonucleotide primers having the nucleic acid sequences as defined according to SEQ ID NO:1-5, SEQ ID NO:31 and SEQ ID NO:32. 